PLVAP

plasmalemma vesicle associated protein

Basic information

Region (hg38): 19:17351450-17377342

Links

ENSG00000130300 ∙ NCBI:83483 ∙ OMIM:607647 ∙ HGNC:13635 ∙ Uniprot:Q9BX97 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diarrhea 10, protein-losing enteropathy type (Moderate), mode of inheritance: AR
• diarrhea 10, protein-losing enteropathy type (Strong), mode of inheritance: AR
• congenital diarrhea 7 with exudative enteropathy (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diarrhea 10, protein-losing enteropathy type	AR	Gastrointestinal	The condition can involve severe protein-losing enteropathy, and awareness may allow early diagnosis and management (eg, with low-fat diet and middle-chain triglyceride-rich formula) which has been reported as beneficial in some individuals	Craniofacial; Gastrointestinal; Genitourinary	26207260; 29661969; 29875123

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLVAP gene.

• not_provided (204 variants)
• Inborn_genetic_diseases (86 variants)
• PLVAP-related_disorder (12 variants)
• Diarrhea_10,_protein-losing_enteropathy_type (8 variants)
• not_specified (2 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLVAP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031310.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	88	7	98
missense	1		109	19	2	131
nonsense	3					3
start loss						0
frameshift	2	2				4
splice donor/acceptor (+/-2bp)			2			2
Total	6	2	114	107	9

Highest pathogenic variant AF is 0.000006160156

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLVAP	protein_coding	protein_coding	ENST00000252590	6	25903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.549	267	293	0.910	0.0000195	2900
Missense in Polyphen		95	109.39	0.86843		1094
Synonymous	-0.984	133	119	1.11	0.00000762	872
Loss of Function	1.66	12	20.0	0.600	0.00000104	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the formation of stomatal and fenestral diaphragms of caveolae. May function in microvascular permeability. {ECO:0000269|PubMed:15155804}.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: MAPK cascade;positive regulation of cellular extravasation;tumor necrosis factor-mediated signaling pathway;protein kinase C signaling
• Cellular component: caveola;cell surface;integral component of membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding;protein homodimerization activity